This report is generated by the tcge-cfmedip-seq-pipeline

Selected QC metrics

  • NOTE: The heatmap is drawn based on transformed Z scores. In general, the darker, the worse! Specifically:
    • raw_reads_depth, usable_reads_depth, saturation_maxEstCor and enrichment_GoGe: the darker, the lower
    • coverage_pctReadsWoCpG and coverage_pctCpGwoRead: the darker, the higher
    • fragment_size_mode: the darker, the further away from the mean mode [only for paired-end reads]

Reads QC metrics

Summary statistics for raw, prefilter and aligned reads

  • raw_reads_depth: number of raw read pairs [Note: it refers to the prefilter_reads for single-end]
  • prefilter_reads: reads or read pairs after QC, adapter trimming and UMI barcode extraction (p.r.n)
  • mapped_reads_pct: percentage of mapped reads or read pairs over the prefileter_reads
  • usable_reads: reads or read pairs after removing the duplication. reads pairs require properly paired as well
  • usable_reads_pct: percentage of usable reads over raw reads
Number of samples: 2
raw_reads_depth prefilter_reads_depth prefilter_reads_pct prefilter_reads_GC prefilter_reads_dedup_pct mapped_reads_pct usable_reads_depth usable_reads_depth_pct
Min 1400000 1399622 99.97 51 92.88 100 1323813 94.56
Q1 1400000 1399622 99.97 51 93.04 100 1324792 94.63
Median 1400000 1399622 99.97 51 93.19 100 1325772 94.70
Mean 1400000 1399622 99.97 51 93.19 100 1325772 94.70
Q3 1400000 1399622 99.97 51 93.35 100 1326752 94.77
Max 1400000 1399622 99.97 51 93.51 100 1327731 94.84

Usable read depth per sample

Usable read depth percentages against raw read depth per sample

Fragment QC metrics

Fragment size Mode, Mean, Median

Number of samples: 2
fragment_size_mode fragment_size_mean fragment_size_median
Min 157 154 156
Q1 157 154 156
Median 157 154 156
Mean 157 154 156
Q3 157 154 156
Max 157 154 156

Fragment size Mode

Fragment size ranges with >=80% properly paired reads

  • Calculated by based on PICARD MEDIAN_INSERT_SIZE + WIDTH_OF_80_PERCENT/2
    • WIDTH_OF_80_PERCENT: The “width” of the bins, centered around the median, that encompass 80% of all read pairs.

MEDIPS QC metrics

Saturation and Coverage Metrics

Number of samples: 2
saturation_maxEstCor coverage_pctReadsWoCpG coverage_pctCpGwoRead coverage_pctCpGw1Read coverage_pctCpGgt5Read
Min 0.98 1.27 89.68 6.590 0.57
Q1 0.98 1.27 89.69 6.605 0.57
Median 0.98 1.27 89.70 6.620 0.57
Mean 0.98 1.27 89.70 6.620 0.57
Q3 0.98 1.27 89.72 6.635 0.57
Max 0.98 1.27 89.73 6.650 0.57

Coverage: percentage of usable reads without CpG, and CpGs without reads

Enrichment score per sample